Thanks for the tips, Paul. It really helped. I noticed in the documentation that the brain was split into left and right thalamus, but there were no instructions on how (or why) to do that. When I tried looking it up, most forums suggested to do some additional step in freesurfer. Is there any other way around that?
Also, when I used the fat_proc_connec_vis in the following way:
fat_proc_connec_vis -in_rois /Users/NET_000_ROI_*.nii.gz -prefix testing -trackid_no_or
and I got the following error messages:
*+ WARNING: output sub-brick 0 is all zeros!
What does this mean ?
*+ WARNING: Set TR of output dataset to 1.0 s
++ elapsed time = 0.3 s
Also this confused me.
Warning SUMA_Make_Edge_List_eng:
Min/Max number of edge hosting triangles: [1/4]
Warning SUMA_Make_Edge_List_eng:
You have edges that belong to more than two triangles.
Bad for analysis assuming surface is a 2-manifold.
Warning SUMA_Make_Edge_List_eng:
Min/Max number of edge hosting triangles: [1/3]
Warning SUMA_Make_Edge_List_eng:
You have edges that belong to more than two triangles.
Bad for analysis assuming surface is a 2-manifold.
Warning SUMA_Make_Edge_List_eng:
Min/Max number of edge hosting triangles: [1/3]
Warning SUMA_Make_Edge_List_eng:
You have edges that belong to more than two triangles.
Bad for analysis assuming surface is a 2-manifold.
I'm not sure what to make of all these errors, what do they mean? I tried to look up the error, for instance, " You have edges that belong to more than two triangles." and I read something about overlapping networks, and how it should be fixed through freesurfer, but I think it just ended up making me a lot more confused.
Also the output files from this command are labelled k1... up until k36, which then are plotted. but from the file names (k1-k36) how am I supposed to know which ROI's the tracts are running through?
I've attached the .niml.dset file screenshot, because I'm not sure if getting all these "NULL"'s at the beginning is normal
